chr2-272926-A-G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000405233.5(ACP1):​c.*668A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.614 in 154,370 control chromosomes in the GnomAD database, including 30,202 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.62 ( 29865 hom., cov: 33)
Exomes 𝑓: 0.53 ( 337 hom. )

Consequence

ACP1
ENST00000405233.5 3_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.112

Publications

14 publications found
Variant links:
Genes affected
ACP1 (HGNC:122): (acid phosphatase 1) The product of this gene belongs to the phosphotyrosine protein phosphatase family of proteins. It functions as an acid phosphatase and a protein tyrosine phosphatase by hydrolyzing protein tyrosine phosphate to protein tyrosine and orthophosphate. This enzyme also hydrolyzes orthophosphoric monoesters to alcohol and orthophosphate. This gene is genetically polymorphic, and three common alleles segregating at the corresponding locus give rise to six phenotypes. Each allele appears to encode at least two electrophoretically different isozymes, Bf and Bs, which are produced in allele-specific ratios. Multiple alternatively spliced transcript variants encoding distinct isoforms have been identified for this gene. [provided by RefSeq, Aug 2008]

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.806 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
ACP1NM_004300.4 linkc.231+776A>G intron_variant Intron 3 of 5 ENST00000272065.10 NP_004291.1 P24666-1Q59EH3
ACP1NM_007099.4 linkc.231+621A>G intron_variant Intron 3 of 5 NP_009030.1 P24666-2
ACP1NR_024080.2 linkn.278+621A>G intron_variant Intron 4 of 6

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ACP1ENST00000272065.10 linkc.231+776A>G intron_variant Intron 3 of 5 1 NM_004300.4 ENSP00000272065.5 P24666-1

Frequencies

GnomAD3 genomes
AF:
0.616
AC:
93582
AN:
151954
Hom.:
29870
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.468
Gnomad AMI
AF:
0.697
Gnomad AMR
AF:
0.530
Gnomad ASJ
AF:
0.598
Gnomad EAS
AF:
0.827
Gnomad SAS
AF:
0.571
Gnomad FIN
AF:
0.759
Gnomad MID
AF:
0.608
Gnomad NFE
AF:
0.691
Gnomad OTH
AF:
0.577
GnomAD4 exome
AF:
0.535
AC:
1229
AN:
2298
Hom.:
337
Cov.:
0
AF XY:
0.534
AC XY:
610
AN XY:
1142
show subpopulations
African (AFR)
AF:
0.378
AC:
28
AN:
74
American (AMR)
AF:
0.444
AC:
8
AN:
18
Ashkenazi Jewish (ASJ)
AF:
1.00
AC:
4
AN:
4
East Asian (EAS)
AC:
0
AN:
0
South Asian (SAS)
AF:
0.564
AC:
53
AN:
94
European-Finnish (FIN)
AC:
0
AN:
0
Middle Eastern (MID)
AF:
0.512
AC:
835
AN:
1632
European-Non Finnish (NFE)
AF:
0.670
AC:
189
AN:
282
Other (OTH)
AF:
0.577
AC:
112
AN:
194
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.483
Heterozygous variant carriers
0
30
60
89
119
149
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Exome Hom
Variant carriers
0
24
48
72
96
120
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome
AF:
0.615
AC:
93598
AN:
152072
Hom.:
29865
Cov.:
33
AF XY:
0.619
AC XY:
46023
AN XY:
74346
show subpopulations
African (AFR)
AF:
0.468
AC:
19389
AN:
41472
American (AMR)
AF:
0.529
AC:
8088
AN:
15280
Ashkenazi Jewish (ASJ)
AF:
0.598
AC:
2075
AN:
3468
East Asian (EAS)
AF:
0.827
AC:
4273
AN:
5166
South Asian (SAS)
AF:
0.569
AC:
2741
AN:
4818
European-Finnish (FIN)
AF:
0.759
AC:
8034
AN:
10584
Middle Eastern (MID)
AF:
0.602
AC:
177
AN:
294
European-Non Finnish (NFE)
AF:
0.691
AC:
46975
AN:
67968
Other (OTH)
AF:
0.574
AC:
1212
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
1774
3548
5321
7095
8869
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
768
1536
2304
3072
3840
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
0.658
Hom.:
46296
Bravo
AF:
0.590
Asia WGS
AF:
0.645
AC:
2242
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
CADD
Benign
0.38
DANN
Benign
0.49
PhyloP100
-0.11
Mutation Taster
=100/0
polymorphism (auto)

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs12714402; hg19: chr2-272926; API